PET/CT scanners offer a hardware solution for aligning and viewing functional and anatomic images that is immune to many of the errors in strictly software registration techniques. Moreover, PET attenuation-corrected emission scans benefit from the use of the onboard CT for fast, low-noise attenuation correction. Along with the significant improved localization and reduced acquisition time, PET/CT scanners also introduce new instrumentation challenges ranging from patient movement to quantitative attenuation correction. This article provides an overview of current PET/CT scanner technology, a discussion of challenges faced by these systems, and pending solutions.